Roots of synthetic ecology: microbes that foster plant resilience in the changing climate

Integration of plant-soil feedbacks with resilience theory for climate change

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.

Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the 'Resilience Revolution'?

Climate change is altering our environment, subjecting multiple agroecosystems worldwide to an increased frequency and intensity of abiotic stress conditions such as heat, drought, flooding, salinity, cold and/or their potential combinations. These stresses impact plant growth, yield and survival, causing losses of billions of dollars to agricultural productivity, and in extreme cases they lead to famine, migration and even wars. As the rate of change in our environment has dramatically accelerated in recent years, more research is urgently needed to discover and develop new ways and tools to increase the resilience of crops to different stress conditions. In this theme issue, new studies addressing the molecular, metabolic, and physiological responses of crops and other plants to abiotic stress challenges are discussed, as well as the potential to exploit these mechanisms in biotechnological applications aimed at preserving and/or increasing crop yield under our changing climate conditions.This article is part of the theme issue 'Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the 'Resilience Revolution'?'

Survival and spread of engineered Mycobacterium smegmatis and associated mycobacteriophage in soil microcosms

The inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread of Mycobacterium smegmatis, engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. Although engineered M. smegmatis and Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than in non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, a higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria, as well as evidence for loss of plasmid over the duration of the experiment, suggests a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments.

IMPORTANCE

Healthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the introduction of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employs Mycobacterium smegmatis as a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges, which must be overcome for successful deployment of engineered microbes in the field.

Integrating 'cry for help' strategies for sustainable agriculture

Plants recruit specific soil microbes through a sophisticated 'cry for help' strategy to mitigate environmental stresses. Recent advances highlight the potential of leveraging this mechanism to develop microbe-based approaches for enhancing crop health, but challenges remain in refining the criteria and conceptual frameworks to effectively investigate and harness these plant-microbe interactions.

A roadmap to understanding and anticipating microbial gene transfer in soil communities

SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

Survival and Spread of Engineered Mycobacterium smegmatis and Associated Mycobacteriophage in Soil Microcosms

The inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread of Mycobacterium smegmatis , engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. While engineered M. smegmatis and Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria as well as evidence for loss of plasmid over the duration of the experiment suggest a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments.

Importance

Healthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the successful deployment of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employs Mycobacterium smegmatis as a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges which must be overcome for successful deployment of engineered microbes in the field.